SangerRead-class-updateQualityParam: updateQualityParam

Description Usage Arguments Value Examples

Description

A SangerRead method which updates QualityReport parameter inside the SangerRead.

Usage

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## S4 method for signature 'SangerRead'
updateQualityParam(object, TrimmingMethod = "M1",
  M1TrimmingCutoff = 1e-04, M2CutoffQualityScore = NULL,
  M2SlidingWindowSize = NULL)

Arguments

object

A SangerRead S4 instance.

TrimmingMethod

The read trimming method for this SangerRead. The value must be "M1" (the default) or 'M2'.

M1TrimmingCutoff

The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the default value is 0.0001. Otherwise, the value must be NULL.

M2CutoffQualityScore

The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2', then the default value is 20. Otherwise, the value must be NULL. It works with M2SlidingWindowSize.

M2SlidingWindowSize

The trimming sliding window size for the Method 2. If TrimmingMethod is 'M2', then the default value is 10. Otherwise, the value must be NULL. It works with M2CutoffQualityScore.

Value

A SangerRead instance.

Examples

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data("sangerReadFData")
updateQualityParam(sangerReadFData,
                   TrimmingMethod         = "M2",
                   M1TrimmingCutoff       = NULL,
                   M2CutoffQualityScore   = 40,
                   M2SlidingWindowSize    = 15)

sangeranalyseR documentation built on Nov. 8, 2020, 5:59 p.m.